ALBANY – A pair of Gov. Andrew Cuomo's aides temporarily will oversee the Thruway Authority as it deals with the abrupt resignation of two top officials that took its board of directors by surprise.

Thruway Executive Director Tom Madison and Chief Financial Officer John Bryan stepped down Wednesday, four weeks after the authority's chairman resigned and 10 days after the Thruway's board passed a budget with a deficit. Jennifer McCormick, Cuomo's deputy director of state operations, will take on the daily operations while Karen Rae, deputy secretary for transportation, will manage the Thruway's transition to new leadership, the authority said.

The resignations come as the Thruway faces increasing scrutiny for its budget shortfall and its plans for tolls on the 570-mile superhighway system. On Dec. 19, the authority passed a $1.7 billion budget that had a revenue shortfall of $25 million, with authority officials declining to say how they will bridge the gap.

Donna Luh, the Thruway's acting chair, said the resignations caught the authority's board by surprise.

"It shocked all of us, actually," Luh said. "(Madison) called me and said they were both submitting resignations and that was that. They were going on with other things in life and other career moves. They didn't discuss that much with me."

Madison was in charge of daily Thruway Authority operations, which include oversight of the toll highway and the state's canal system. He was appointed by Cuomo in 2011. In a brief statement, Madison said it was a "particular privilege" to work at the Thruway Authority as it began work on a $3.9 billion replacement for the Tappan Zee Bridge between Westchester and Rockland.

"It has been an honor to serve in Governor Cuomo's administration as executive director of the Thruway Authority and Canal Corporation during such a pivotal time in the history of the organization," Madison said.

Cuomo's administration and the Thruway Authority continue to face questions about the funding of the Tappan Zee Bridge project and whether a highway toll increase can be avoided to bridge the authority's budget gap. More than 95 percent of the Thruway's revenue comes from tolls.

Luh said the board did not request either resignation, which came amid reports that the state Inspector General's office is in the midst of a probe of the Thruway's operations. She said she had "no problems" with Madison's work. She said she didn't know whether the Madison and Bryan resignations were forced by Cuomo's office. Luh said she has not been contacted by the Inspector General's office.

"I have no idea," Luh said. "But it certainly didn't seem like that at all."